Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01014904.1 Kokia drynarioides strain JFW-HI SEQ_129947, whole genome shotgun sequence

Parameters: 2 7 7 80 10 50 1000

Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000

Length: 15710
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34


Found at i:5729 original size:12 final size:12

Alignment explanation


    Indices: 5694--5756  Score: 51
    Period size: 12  Copynumber: 5.3  Consensus size: 12

       5684 AACTTAATCA

                      * 
       5694 AACATGTTCACG
          1 AACATGTTCATG

                         
       5706 AACAT-TAT-ATG
          1 AACATGT-TCATG

                        
       5717 AACATGTTCATG
          1 AACATGTTCATG

                  * *    
       5729 AACAT-ATAATTG
          1 AACATGTTCA-TG

                      * 
       5741 AACATGTTCACG
          1 AACATGTTCATG

                
       5753 AACA
          1 AACA

       5757 ATATTAATGA


Statistics
Matches: 40,  Mismatches: 6, Indels: 10
        0.71            0.11        0.18

Matches are distributed among these distances:
  11   11  0.28
  12   27  0.68
  13    2  0.05

ACGTcount: A:0.41, C:0.17, G:0.13, T:0.29


Consensus pattern (12 bp):   
AACATGTTCATG

Found at i:5747 original size:24 final size:23

Alignment explanation


    Indices: 5694--5756  Score: 92
    Period size: 24  Copynumber: 2.7  Consensus size: 23

       5684 AACTTAATCA

                                   
       5694 AACATGTTCACGAACATTATATG
          1 AACATGTTCACGAACATTATATG

                      *              
       5717 AACATGTTCATGAACA-TATAATTG
          1 AACATGTTCACGAACATTAT-A-TG

                            
       5741 AACATGTTCACGAACA
          1 AACATGTTCACGAACA

       5757 ATATTAATGA


Statistics
Matches: 36,  Mismatches: 2, Indels: 3
        0.88            0.05        0.07

Matches are distributed among these distances:
  22    3  0.08
  23   16  0.44
  24   17  0.47

ACGTcount: A:0.41, C:0.17, G:0.13, T:0.29


Consensus pattern (23 bp):   
AACATGTTCACGAACATTATATG

Found at i:5784 original size:25 final size:23

Alignment explanation


    Indices: 5753--5808  Score: 62
    Period size: 22  Copynumber: 2.4  Consensus size: 23

       5743 CATGTTCACG

                        *           
       5753 AACAATATTAATGAATAACAAACA
          1 AACAATATTAATAAATAA-AAACA

                                   
       5777 AACAA-A-TAATAAATAAAAACA
          1 AACAATATTAATAAATAAAAACA

            *          
       5798 CACAAATATTA
          1 AAC-AATATTA

       5809 TTTTAATATT


Statistics
Matches: 27,  Mismatches: 2, Indels: 6
        0.77            0.06        0.17

Matches are distributed among these distances:
  21    7  0.26
  22   11  0.41
  23    2  0.07
  24    7  0.26

ACGTcount: A:0.66, C:0.12, G:0.02, T:0.20


Consensus pattern (23 bp):   
AACAATATTAATAAATAAAAACA

Found at i:5802 original size:21 final size:22

Alignment explanation


    Indices: 5761--5805  Score: 65
    Period size: 21  Copynumber: 2.1  Consensus size: 22

       5751 CGAACAATAT

                *                 
       5761 TAATGAATAACAAACAAACAAA
          1 TAATAAATAACAAACAAACAAA

                            *     
       5783 TAATAAATAA-AAACACACAAA
          1 TAATAAATAACAAACAAACAAA

              
       5804 TA
          1 TA

       5806 TTATTTTAAT


Statistics
Matches: 21,  Mismatches: 2, Indels: 1
        0.88            0.08        0.04

Matches are distributed among these distances:
  21   12  0.57
  22    9  0.43

ACGTcount: A:0.69, C:0.13, G:0.02, T:0.16


Consensus pattern (22 bp):   
TAATAAATAACAAACAAACAAA

Found at i:11016 original size:78 final size:77

Alignment explanation


    Indices: 10922--11083  Score: 236
    Period size: 78  Copynumber: 2.1  Consensus size: 77

      10912 TTATTTTTAC

                *                                                            
      10922 ATATTACTCACAAAAAAATCAGTTAATGGATTTAATGACTATTATTTAAATTAAGACTAAAATTT
          1 ATATAACTCACAAAAAAATCAGTTAATGGATTTAATGACTATTATTTAAA-TAAGACTAAAATTT

            *             
      10987 TGAAATTAAAAAAA
         65 CGAAATT-AAAAAA

                                                  *    *             *       
      11001 ATATAACTCAC-AAAAAATCAGTTAATGGATTTAATGATTATTGTTTAAATAAGACTTAAATTTC
          1 ATATAACTCACAAAAAAATCAGTTAATGGATTTAATGACTATTATTTAAATAAGACTAAAATTTC

                  * *   
      11065 GAAATTCAGAAA
         66 GAAATTAAAAAA

                   
      11077 ATATAAC
          1 ATATAAC

      11084 AACAAAGAAT


Statistics
Matches: 76,  Mismatches: 7, Indels: 3
        0.88            0.08        0.03

Matches are distributed among these distances:
  76   11  0.14
  77   19  0.25
  78   36  0.47
  79   10  0.13

ACGTcount: A:0.49, C:0.09, G:0.09, T:0.34


Consensus pattern (77 bp):   
ATATAACTCACAAAAAAATCAGTTAATGGATTTAATGACTATTATTTAAATAAGACTAAAATTTC
GAAATTAAAAAA

Found at i:11263 original size:31 final size:30

Alignment explanation


    Indices: 11225--11295  Score: 83
    Period size: 30  Copynumber: 2.4  Consensus size: 30

      11215 AAAAATAAAA

                           *            *  
      11225 AAAACTAAAATTG-ACCAATTCAAAAAATAT
          1 AAAACTAAAATTGAAACAATT-AAAAAACAT

                                      *    
      11255 AAAGACTAAAA-TGAAACAATTAAAATACAT
          1 AAA-ACTAAAATTGAAACAATTAAAAAACAT

                       
      11285 AAAACTAAAAT
          1 AAAACTAAAAT

      11296 CACAAAATCA


Statistics
Matches: 35,  Mismatches: 3, Indels: 6
        0.80            0.07        0.14

Matches are distributed among these distances:
  29    7  0.20
  30   15  0.43
  31   13  0.37

ACGTcount: A:0.63, C:0.11, G:0.04, T:0.21


Consensus pattern (30 bp):   
AAAACTAAAATTGAAACAATTAAAAAACAT
Done.